[English] 日本語
Yorodumi
- PDB-1t0w: 25 NMR structures of Truncated Hevein of 32 aa (Hevein-32) comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1t0w
Title25 NMR structures of Truncated Hevein of 32 aa (Hevein-32) complex with N,N,N-triacetylglucosamina
ComponentsHevein
KeywordsSUGAR BINDING PROTEIN / alpha-helix / anti-parallel beta-sheet
Function / homology
Function and homology information


chitin binding / RNA nuclease activity / defense response to fungus / defense response to bacterium
Similarity search - Function
Barwin domain / Barwin, conserved site / Pathogenesis-related protein-4 / Barwin family / Barwin domain signature 1. / Barwin domain signature 2. / Barwin domain profile. / Chitin-binding, type 1, conserved site / Chitin recognition protein / Chitin recognition or binding domain signature. ...Barwin domain / Barwin, conserved site / Pathogenesis-related protein-4 / Barwin family / Barwin domain signature 1. / Barwin domain signature 2. / Barwin domain profile. / Chitin-binding, type 1, conserved site / Chitin recognition protein / Chitin recognition or binding domain signature. / Chitin-binding type-1 domain profile. / Chitin binding domain / Chitin-binding, type 1 / Endochitinase-like superfamily / RlpA-like domain superfamily
Similarity search - Domain/homology
triacetyl-beta-chitotriose / Pro-hevein
Similarity search - Component
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsAboitiz, N. / Vila-Perello, M. / Groves, P. / Asensio, J.L. / Andreu, D. / Canada, F.J. / Jimenez-Barbero, J.
Citation
Journal: Chembiochem / Year: 2004
Title: NMR and modeling studies of protein-carbohydrate interactions: synthesis, three-dimensional structure, and recognition properties of a minimum hevein domain with binding affinity for chitooligosaccharides
Authors: Aboitiz, N. / Vila-Perello, M. / Groves, P. / Asensio, J.L. / Andreu, D. / Canada, F.J. / Jimenez-Barbero, J.
#1: Journal: Eur.J.Biochem. / Year: 1995
Title: The interaction of hevein with N-acetylglucosamine-containing oligosaccharides. Solution structure of hevein complexed to chitobiose
Authors: Asensio, J.L. / Canada, F.J. / Bruix, M. / Rodriguez-Romero, A. / Jimenez-Barbero, J.
#2: Journal: J.Mol.Biol. / Year: 1996
Title: H NMR study of the solution structure of Ac-AMP2, a sugar binding antimicrobial protein isolated from amaranthus caudatus
Authors: Martins, J.C. / Maes, D. / Loris, R. / Pepermans, H.A. / Wyns, L. / Willem, R. / Verheyden, P.
#3: Journal: Glycobiology / Year: 1998
Title: NMR investigations of protein-carbohydrate interactions: refined three-dimensional structure of the complex between hevein and methyl beta-chitobioside
Authors: Asensio, J.L. / Canada, F.J. / Bruix, M. / Gonzalez, C. / Khiar, N. / Rodriguez-Romero, A. / Jimenez-Barbero, J.
#4: Journal: PROTEINS: STRUCT.,FUNCT.,GENET. / Year: 2000
Title: NMR Investigations of Protein-Carbohydrate Interactions: Studies on the Relevance of Trp/Tyr Variations in Lectin Binding Sites as Deduced from Titration Microcalorimetry and NMR Studies on ...Title: NMR Investigations of Protein-Carbohydrate Interactions: Studies on the Relevance of Trp/Tyr Variations in Lectin Binding Sites as Deduced from Titration Microcalorimetry and NMR Studies on Hevein Domains. Determination of the NMR Structure of the Complex between Pseudohevein and N'N',N''-triacetylchitotriose
Authors: Asensio, J.L. / Siebert, H.-C. / von der Lieth, C.-W. / Laynez, J. / Bruix, M. / Soedjanaamadja, U.M. / Beintema, J.J. / Canada, F.J. / Gabius, H.-J. / Jimenez-Barbero, J.
#5: Journal: Chem.Biol. / Year: 2000
Title: Structural basis for chitin recognition by defense proteins: GlcNAc residues are bound in a multivalent fashion by extended binding sites in hevein domains
Authors: Asensio, J.L. / Canada, F.J. / Siebert, H.-C. / Laynez, J. / Poveda, A. / Nieto, P.M. / Soedjanaamadja, U.M. / Gabius, H.-J. / Jimenez-Barbero, J.
History
DepositionApr 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hevein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1122
Polymers3,4851
Non-polymers6281
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 25all calculated structures submitted
RepresentativeModel #1fewest violations

-
Components

#1: Protein/peptide Hevein / ALLERGEN HEV B 6


Mass: 3484.858 Da / Num. of mol.: 1 / Fragment: N-terminal domain / Source method: obtained synthetically
Details: Sequence prepared on a MBHA resin by standard solid phase peptide synthesis protocols. The SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN HEVEA BRASILIENSIS (PARA RUBBER TREE).
References: UniProt: P02877
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques at tm = 200 and 300 ms

-
Sample preparation

DetailsContents: 0.5 mM hev32, 3 mM chitotriose, 20 mM phosphate buffer, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100 mM NaCl / pH: 5.6 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

-
Processing

NMR software
NameVersionClassification
XwinNMR3.2collection
XEASY1.3.13data analysis
DIANA1.5structure solution
Amber5refinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: The structures are based on a total of 339 restraints: 321 are NOE-derived distance constraints and 18 come from cys-cys disulfide bridges
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 25 / Conformers submitted total number: 25

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more